Genome sequence analysis of the Vibrio parahaemolyticus lytic bacteriophage VPMS1

Abstract

VPMS1 is a Vibrio parahaemolyticus lytic phage isolated from a marine clam. The 42.3-kb genome was predicted to encode 53 proteins. Comparison of the VPMS1 DNA genome with known phage genomes revealed no similarity; hence, it represents a new VP phage, organized into three differently oriented modules. The module for packaging covers 12 % of the genome, the module for structure covers 31 %, and the module for replication and regulation covers 48 %. The G + C content was 44.67 %. The coding region corresponds to 91 % of the genome, and 9 % apparently does not encode any protein. Thirty genes, constituting 57 % of the genome, had significant similarity to some reported proteins in the protein database; 23 genes, constituting 43 % of the genome, showed no significant homology to any reported protein, and these could be new proteins whose hypothetical functions can be deduced from their position in the genome.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. 1.

    Matsuda S, Kodama T, Okada N, Okayama K, Honda T, Iida T (2010) Association of Vibrio parahaemolyticus thermostable direct hemolysin with lipid rafts is essential for cytotoxicity but not hemolytic activity. Infect Immun 78:603–610

    PubMed  Article  CAS  Google Scholar 

  2. 2.

    Sakata J, Kawatsu K, Kawahara R, Kanki M, Iwasaki T, Kumeda Y, Kodama H (2012) Production and characterization of a monoclonal antibody against recombinant thermolabile hemolysin and its application to screen for Vibrio parahaemolyticus contamination in raw seafood. Food Control 23:171–176

    Article  CAS  Google Scholar 

  3. 3.

    Mahoney J, Gerding M, Jones S, Whistler C (2010) Comparison of the pathogenic potentials of environmental and clinical Vibrio parahaemolyticus strains indicates a role for temperature regulation virulence. Appl Environ Microbiol 76:7459–7465

    PubMed  Article  CAS  Google Scholar 

  4. 4.

    Goarant C, Merien F, Berthe F, Mermoud I, Perolat P (1999) Arbitrarily primed PCR to type Vibrio spp. Pathogenic for shrimp. Appl Environ Microbiol 65:1145–1151

    PubMed  CAS  Google Scholar 

  5. 5.

    De Paola A, Nordstrom J, Bowers J, Wells J, Cook D (2003) Seasonal abundance of total and pathogenic Vibrio parahaemolyticus in Alabama oysters. Appl Environ Microbiol 69:1521–1526

    Article  Google Scholar 

  6. 6.

    Ward L, Bej A (2006) Detection of Vibrio parahaemolyticus in shellfish by use of multiplexed real time PCR with TaqMan fluorescent probes. Appl Environ Microbiol 72:2031–2042

    PubMed  Article  CAS  Google Scholar 

  7. 7.

    Parisien A, Allain B, Zhang J, Mandeville R, Lan C (2007) Novel alternatives to antibiotics: bacteriophages, bacterial cell wall hydrolases, and antimicrobial peptides. J Appl Microbiol 104:1–13

    Google Scholar 

  8. 8.

    Martínez-Díaz SF, Hipólito-Morales A (2013) Efficacy of phage therapy to prevent mortality during vibriosis of brine shrimp. Aquaculture. doi:10.1016/j.aquaculture.2013.03.007

  9. 9.

    Kropinski A, Mazzocco A, Waddell T, Lingohr E, Johnson R (2009) Enumeration of bacteriophages by double agar overlay plaque assay. In: Clokie M, Kropinski A (eds) Bacteriophages: methods and protocols. Humana Press, New York, pp 69–76

    Google Scholar 

  10. 10.

    Carlson K (2005) Working with bacteriophages: common techniques and methodological approaches. In: Kutter E, Sulakvelidze A (eds). Bacteriophages: biology and application. CRC Press, Boca Raton, pp 437–494

  11. 11.

    Sambrock J, Rusell D (2001) Molecular cloning: a laboratory manual, vol 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

  12. 12.

    Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucl Acids Res 33:W451–W454

    PubMed  Article  CAS  Google Scholar 

  13. 13.

    Punta M, Coggill P, Eberhardt R et al (2012) The Pfam protein families. Nucleic Acids Res 40:D290–D301

    PubMed  Article  CAS  Google Scholar 

  14. 14.

    Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:686–689

    Article  Google Scholar 

  15. 15.

    Laslett D, Canback B (2004) ARAGORN, a program for the detection of transfer RNA and transfer-messenger RNA genes. Nucl Acids Res 32:11–16

    PubMed  Article  CAS  Google Scholar 

  16. 16.

    Han H, Hinh-Chung W, Kan B, Guo Z, Zeng X, Yin S, Liu X, Yang R, Zhou D (2008) Genome plasticity of Vibrio parahaemolyticus: microevolution of the pandemic group. BMC Genomics. doi:10.1186/1471-2164-9-570

    Google Scholar 

  17. 17.

    Bailly-Bechet M, Vergassola M, Rocha E (2007) Causes for the intriguing presence of tRNAs. Genome Res 17:1486–1495

    PubMed  Article  CAS  Google Scholar 

  18. 18.

    Lin Y, Lin C (2012) Genome-wide characterization of Vibrio phage Phi-pp 2 with unique arrangements of the mob-like genes. Bio Med Central Genomics. doi:10.1186/1471-2164-13-224

    Google Scholar 

  19. 19.

    Brüssow H (2006) Prophage genomics. In: Calendar R, Abedon ST (eds) The Bacteriophages, 2nd edn. Oxford University Press, Oxford, pp 17–25

    Google Scholar 

Download references

Acknowledgments

We thank Ira Fogel of Centro de Investigaciones Biológicas del Noroeste, for editorial services, and Diana Barajas for assistance with phage selection, Lina Zermeño for phage production, and Victor Moyrón for technical support. Funding was provided by Consejo Nacional de Ciencia y Tecnología of México (CONACYT grants 52107 and 85033).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Martín Ramírez-Orozco.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ramírez-Orozco, M., Serrano-Pinto, V., Ochoa-Álvarez, N. et al. Genome sequence analysis of the Vibrio parahaemolyticus lytic bacteriophage VPMS1. Arch Virol 158, 2409–2413 (2013). https://doi.org/10.1007/s00705-013-1726-3

Download citation

Keywords

  • Phage Genome
  • Lytic Phage
  • Vibrio Parahaemolyticus
  • Hypothetical Function
  • Agar Double Layer